One of the new features in El Capitan is the Security Integrity Protection (also called rootless), which is just a fancy way of saying that system files cannot be added, edited, or deleted while the feature is turned on. This means that you cannot change icons for system programs, such as Safari, Messages, and iTunes. So while the main process of changing icons in El Capitan is the same as with previous versions of OS X, you first have to turn off SIP.

It is worth noting that the process outlines below is only necessary when changing system application icons. For any other application it is not needed.

Turn Off SIP

Turn off your Mac
Turn it back on and hold ⌘-R until the Apple logo with a progress bar pops up, this boots your Mac into Recovery Mode
Click “Utilities” in the menu bar, and select Terminal
Type the command csrutil status in order to check whether SIP is enabled or disabled.
If enabled, type csrutil disable, this will turn off SIP
Click the  in the menu bar and select Restart
Change Icons

Since SIP is turned off now, you can change icons! If you already know how to do this part you can skip to the next section (it is the same process as with previous OS X releases).

To change the icon of an application:

Open a Finder window and go to the folder where the new icon is located
Open a new Finder window
Open the Applications folder
Find the application you want to change the icon for
Either right-click on the application and choose “Get Info”, or hit ⌘-I
Now simply drag the new icon onto the icon image in the Info window (as seen in the image below)

If this application is a system application (anything bundled with OS X like Calendar, Reminders, etc.) you will have to enter your password to allow the change

Congratulations! That application’s icon is much prettier now!
In order to see the changes in your dock, open Terminal and enter killall Dock to restart the dock.

Change the Finder Icon

Changing the Finder icon is a more involved process than with other applications.

If the file you want to use as the new icon is a .icns file, change the extension of the file to .png. This can be done by renaming the file
Open a new Finder window and enter the shortcut Command-Shift-G
Paste this address into the dialog and click “Go” /System/Library/CoreServices/Dock.app/Contents/Resources/
Find and copy the finder.png and finder@2x.png files into a backup location
Remove the finder.png and finder@2x.png files from the folder
Move your new icon (with the .png extension) into the Resources folder, you will have to authenticate with your password
Hit Command-Shift-G again and go to this new address /private/var/folders/
Now search for “com.apple.dock.iconcache” and delete the file once it is found
Open Terminal and enter the command killall Dock to restart your dock. Your new Finder icon should show up!
Turn On SIP

Now that you have finished updating the icons that you would like to update, you should turn SIP back on. This process is the same as turning it off, except you will use the csrutil enable command to turn SIP on. I have listed the steps below if you don’t want to scroll back to the top again.

Turn off your Mac
Turn it back on and hold ⌘-R until the Apple logo with a progress bar pops up, this boots your Mac into Recovery Mode
Click “Utilities” in the menu bar, and select Terminal
Use the command csrutil status in order to check whether SIP is enabled or disabled.
If disabled, type csrutil enable, this will turn on SIP
Click the  in the menu bar and select Restart
Enjoy Your New Dock!

I’m not a huge fan of the stock icons for OS X, especially after the design refresh of Yosemite. That’s why I choose to customize the icons of applications on my Mac. I really love the icons made by the wonderful Ollin Bohan, which can be downloaded from his website here.

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